Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007499.1 Hibiscus syriacus cultivar Beakdansim tig00020782_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 100444
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2956 original size:13 final size:12
Alignment explanation
Indices: 2901--2984 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 12
2891 ATATAGGCGT
2901 GATATGGTGATG
1 GATATGGTGATG
2913 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2925 GATA-GGCG-T-
1 GATATGGTGATG
2934 GATAATGGTGATG
1 GAT-ATGGTGATG
2947 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2959 GATATAGGCG-T-
1 GATAT-GGTGATG
2970 GATAATGGTGATG
1 GAT-ATGGTGATG
2983 GA
1 GA
2985 CAGATTGTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 16 0.28
12 11 0.19
13 22 0.38
14 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2973 original size:36 final size:36
Alignment explanation
Indices: 2883--2985 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2873 ATTTATAAGT
* *
2883 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2918 TGGTGATG--ATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2952 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2986 AGATTGTATC
Statistics
Matches: 63, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
33 11 0.17
34 21 0.33
35 7 0.11
36 24 0.38
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:4671 original size:11 final size:12
Alignment explanation
Indices: 4647--4675 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4637 TACTTTATCT
4647 TATATTTACTTA
1 TATATTTACTTA
4659 TATATTTAC-TA
1 TATATTTACTTA
4670 TATATT
1 TATATT
4676 ATTATGAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATTTACTTA
Found at i:5102 original size:15 final size:16
Alignment explanation
Indices: 5062--5107 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
5052 AATATTTTAA
*
5062 TATAGTTATTTTGATC
1 TATAGTTATTATGATC
*
5078 TACA-TATATTAT-ATC
1 TATAGT-TATTATGATC
5093 TATAGTTATTATGAT
1 TATAGTTATTATGAT
5108 GATAACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (16 bp):
TATAGTTATTATGATC
Found at i:6383 original size:19 final size:20
Alignment explanation
Indices: 6367--6402 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
6357 CTTTATTTCA
6367 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
6386 TTTCATTACTTA-TATTT
1 TTTCATTACTTATTATTT
6403 TTATCCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:6639 original size:10 final size:11
Alignment explanation
Indices: 6615--6639 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6605 ATTGGCGTGC
6615 AAAACAGAAGA
1 AAAACAGAAGA
6626 AAAACAGAAGA
1 AAAACAGAAGA
6637 AAA
1 AAA
6640 GACTCCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAACAGAAGA
Found at i:6724 original size:19 final size:19
Alignment explanation
Indices: 6668--6726 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
6658 GGAGTGCAAA
*
6668 AAGAAAGGAAAAGAGAAAAG
1 AAGAAAAGAAAAGA-AAAAG
*
6688 AAGAGAAA-AATCAG-AAAAG
1 AAGA-AAAGAA-AAGAAAAAG
6707 AAGAAAAGAAAAGAAAAAG
1 AAGAAAAGAAAAGAAAAAG
6726 A
1 A
6727 GAAGTTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 5 0.16
19 17 0.53
20 6 0.19
21 4 0.12
ACGTcount: A:0.73, C:0.02, G:0.24, T:0.02
Consensus pattern (19 bp):
AAGAAAAGAAAAGAAAAAG
Found at i:17641 original size:14 final size:13
Alignment explanation
Indices: 17622--17671 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
17612 AAGAAAAAAG
17622 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
17636 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
17649 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
17660 AAAGAAAAAGAA
1 AAAGAAAAAGAA
17672 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:17668 original size:19 final size:18
Alignment explanation
Indices: 17611--17671 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
17601 ATTGGCGTAC
17611 AAAGAAAAAAG-AAAGAA
1 AAAGAAAAAAGAAAAGAA
17628 AAAGACAAAAAGAAGAAG-A
1 AAAGA-AAAAAGAA-AAGAA
17647 AAAGAAGAAAAGAAAAGAA
1 AAAGAA-AAAAGAAAAGAA
17666 AAAGAA
1 AAAGAA
17672 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 5 0.13
18 10 0.26
19 21 0.54
20 3 0.08
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAGAA
Found at i:17688 original size:11 final size:10
Alignment explanation
Indices: 17611--17671 Score: 51
Period size: 10 Copynumber: 6.2 Consensus size: 10
17601 ATTGGCGTAC
17611 AAAGAAAAAAG
1 AAAG-AAAAAG
17622 AAAGAAAAAG
1 AAAGAAAAAG
17632 ACAA-AAAGAAG
1 A-AAGAAA-AAG
17643 -AAG-AAAAG
1 AAAGAAAAAG
17651 -AAG-AAAAG
1 AAAGAAAAAG
17659 AAAAGAAAAAG
1 -AAAGAAAAAG
17670 AA
1 AA
17672 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
8 11 0.25
9 4 0.09
10 15 0.34
11 14 0.32
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:26167 original size:5 final size:6
Alignment explanation
Indices: 26145--26177 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
26135 TGTACTTCTC
26145 TTTTTG TATTTTG TTTTTG TTTTTG TTTTTG TT
1 TTTTTG T-TTTTG TTTTTG TTTTTG TTTTTG TT
26178 GTACGTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (6 bp):
TTTTTG
Found at i:28487 original size:35 final size:35
Alignment explanation
Indices: 28407--28526 Score: 152
Period size: 35 Copynumber: 3.4 Consensus size: 35
28397 AAGATACTAT
*
28407 CTAT-TCATCACCATCTTCCATCACCACTTTCTCGC
1 CTATATCATCACCATCTTCCATCACCA-TTTCACGC
* * *
28442 CTATAACATCACCATCTTCCATCATCATTGCACGC
1 CTATATCATCACCATCTTCCATCACCATTTCACGC
* * * *
28477 CTATATCATCACCATATTCTATCACCATTTCATGT
1 CTATATCATCACCATCTTCCATCACCATTTCACGC
28512 CTATATCATCACCAT
1 CTATATCATCACCAT
28527 TCCTTAACCA
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 53 0.73
36 20 0.27
ACGTcount: A:0.27, C:0.36, G:0.03, T:0.34
Consensus pattern (35 bp):
CTATATCATCACCATCTTCCATCACCATTTCACGC
Found at i:28933 original size:15 final size:16
Alignment explanation
Indices: 28894--28947 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
28884 TGCTGCAACG
*
28894 AAAAGAAAAAGAAAGAA
1 AAAAG-AAAAGAAAAAA
** *
28911 TGAAGAAAA-AACAAA
1 AAAAGAAAAGAAAAAA
28926 AAAAGAAAAGAAAAAA
1 AAAAGAAAAGAAAAAA
28942 AAAAGA
1 AAAAGA
28948 CTCCTACATC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 11 0.38
16 15 0.52
17 3 0.10
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAA
Found at i:32728 original size:15 final size:15
Alignment explanation
Indices: 32717--32745 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
32707 ACTCAAAAAG
32717 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
32732 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
32746 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:35504 original size:11 final size:13
Alignment explanation
Indices: 35472--35501 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35462 TGGCGAAAGA
35472 TGAAAAGGTATGT
1 TGAAAAGGTATGT
35485 TGAAAAGGTATG-
1 TGAAAAGGTATGT
35497 TGAAA
1 TGAAA
35502 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:50500 original size:24 final size:21
Alignment explanation
Indices: 50466--50509 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
50456 TCCACAAGAT
*
50466 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
50488 ATGTACCTCTTGAAATTCAAAG
1 ATGT-CCT-TTGAAATTCAAAG
50510 AATGACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:51875 original size:36 final size:36
Alignment explanation
Indices: 51783--51887 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
51773 ATTTATAAGT
* * **
51783 TGGTGATAATATAAGCGTGAT-ATGACGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
51818 TGGTGATGATATAGGCATGATAATGGTGATGGACA-A
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA-ATA
51854 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAA
51888 AGATTGTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 19 0.31
36 42 0.68
37 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:57554 original size:13 final size:12
Alignment explanation
Indices: 57535--57620 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
57525 ATATAGGCGT
57535 GATATGGTGATG
1 GATATGGTGATG
57547 GAATATGGTGAT-
1 G-ATATGGTGATG
57559 GATATAGGTG-T-
1 GATAT-GGTGATG
57570 GATAATGGTGATG
1 GAT-ATGGTGATG
57583 GACTATGGTGAT-
1 GA-TATGGTGATG
*
57595 GATATAGGCG-T-
1 GATAT-GGTGATG
57606 GATAATGGTGATG
1 GAT-ATGGTGATG
57619 GA
1 GA
57621 CAGATTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 17 0.27
13 22 0.35
14 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:57572 original size:11 final size:12
Alignment explanation
Indices: 57518--57602 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 12
57508 TTTATAAGTT
*
57518 GGTGATAATATA
1 GGTGATGATATA
*
57530 GGCG-TGATAT-
1 GGTGATGATATA
57540 GGTGATGGA-ATA
1 GGTGAT-GATATA
57552 TGGTGATGATATA
1 -GGTGATGATATA
57565 GGTG-TGATA-A
1 GGTGATGATATA
57575 TGGTGATGGACTAT-
1 -GGTGAT-GA-TATA
57589 GGTGATGATATA
1 GGTGATGATATA
57601 GG
1 GG
57603 CGTGATAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
10 4 0.07
11 20 0.34
12 16 0.27
13 17 0.29
14 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:57590 original size:36 final size:36
Alignment explanation
Indices: 57517--57621 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
57507 ATTTATAAGT
* *
57517 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
57552 TGGTGATGATATAGGTGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
57588 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
57622 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:61281 original size:13 final size:13
Alignment explanation
Indices: 61262--61297 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
61252 TCCAACACTC
61262 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
61275 GAAAAGAAAAGAA
1 AAAAAGAAAAGAA
61288 AAGAAAGAAA
1 AA-AAAGAAA
61298 GAATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:65698 original size:36 final size:37
Alignment explanation
Indices: 65651--65740 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 37
65641 AGATACAATC
65651 TGTCCATCACCATTATCACACCTATATCATCACCAT-
1 TGTCCATCACCATTATCACACCTATATCATCACCATA
* *
65687 TGTCCATCACCATTATCACGCCTATATCATCACTATA
1 TGTCCATCACCATTATCACACCTATATCATCACCATA
65724 T-TCCATCACCA-TATCAC
1 TGTCCATCACCATTATCAC
65741 GCCAATAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
35 6 0.12
36 44 0.86
37 1 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (37 bp):
TGTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:65768 original size:33 final size:33
Alignment explanation
Indices: 65724--65792 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
65714 CATCACTATA
65724 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCGCCAATAA-ATCATCC
* * * *
65757 TTCCATTACCATTTCATCTCCATTAAATCATCC
1 TTCCATCACCATATCATCGCCAATAAATCATCC
65790 TTC
1 TTC
65793 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.29, C:0.36, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCGCCAATAAATCATCC
Found at i:70171 original size:35 final size:36
Alignment explanation
Indices: 70072--70171 Score: 129
Period size: 33 Copynumber: 2.9 Consensus size: 36
70062 AGATACAATC
70072 TGTCCATCACCATTATCACGCCTATATCATCACCAT
1 TGTCCATCACCATTATCACGCCTATATCATCACCAT
*
70108 TGT-C--CACCATTATCACGCCTATATCATCACTAT
1 TGTCCATCACCATTATCACGCCTATATCATCACCAT
* *
70141 AT-TCCATCACCA-TATCACGCCAATAACATCA
1 -TGTCCATCACCATTATCACGCCTATATCATCA
70172 TCCTTCCATT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
33 29 0.51
34 2 0.04
35 18 0.32
36 8 0.14
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
TGTCCATCACCATTATCACGCCTATATCATCACCAT
Found at i:73174 original size:11 final size:12
Alignment explanation
Indices: 73144--73192 Score: 57
Period size: 11 Copynumber: 4.2 Consensus size: 12
73134 TTGGTGCTGG
73144 AAACAAGATAAA
1 AAACAAGATAAA
* *
73156 AAATAAGAT-TA
1 AAACAAGATAAA
73167 AAACAAGATAAA
1 AAACAAGATAAA
*
73179 GAA-AAGATAAA
1 AAACAAGATAAA
73190 AAA
1 AAA
73193 TTGCAAATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.12
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:73192 original size:23 final size:23
Alignment explanation
Indices: 73144--73191 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
73134 TTGGTGCTGG
*
73144 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAATAAGATAA
*
73167 AAACAAGATAAAGAA-AAGATAA
1 AAACAAGATAAAAAATAAGATAA
73189 AAA
1 AAA
73192 ATTGCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.12
Consensus pattern (23 bp):
AAACAAGATAAAAAATAAGATAA
Found at i:79103 original size:19 final size:20
Alignment explanation
Indices: 79079--79130 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
79069 CGGCCAAGAG
* *
79079 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
79098 CATGTATTTTCATCAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
79119 CATGTATTTTCA
1 CATGTATTTTCA
79131 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:79550 original size:19 final size:16
Alignment explanation
Indices: 79526--79585 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 16
79516 TTAGAGTGCA
79526 AAAAGAAGAGAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
*
79545 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
79561 AAAAGAAGAAAAGAAAAG
1 AAAAGAAG-AAA-AAAAG
79579 AAAAGAA
1 AAAAGAA
79586 AAAGAGAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.27
17 3 0.08
18 15 0.41
19 9 0.24
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:79554 original size:8 final size:8
Alignment explanation
Indices: 79543--79594 Score: 70
Period size: 8 Copynumber: 6.2 Consensus size: 8
79533 GAGAAAAATC
79543 AGAAAAGA
1 AGAAAAGA
79551 AGAAAAGA
1 AGAAAAGA
79559 AGAAAAGA
1 AGAAAAGA
79567 AGAAAAGAAA
1 AGAAAAG--A
79577 AGAAAAGA
1 AGAAAAGA
79585 A-AAAGAGA
1 AGAAA-AGA
79593 AG
1 AG
79595 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
7 3 0.08
8 29 0.73
10 8 0.20
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:79566 original size:13 final size:13
Alignment explanation
Indices: 79550--79585 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
79540 ATCAGAAAAG
79550 AAGAAAAGAAGAA
1 AAGAAAAGAAGAA
79563 AAGAAGAA-AAGAA
1 AAGAA-AAGAAGAA
79576 AAGAAAAGAA
1 AAGAAAAGAA
79586 AAAGAGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAAGAA
Found at i:79590 original size:6 final size:5
Alignment explanation
Indices: 79550--79587 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
79540 ATCAGAAAAG
79550 AAGAA AAGAA GAA-AA GAAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA -AAGAA -AAGAA AAGAA AAGAA AAGAA AA
79588 AGAGAAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:82057 original size:30 final size:31
Alignment explanation
Indices: 82005--82064 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
81995 CTTAGCTTTA
**
82005 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
82035 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
82065 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:82993 original size:20 final size:20
Alignment explanation
Indices: 82968--83006 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
82958 TATCTTCATT
82968 AAAATCATGTATTTTCAAAA
1 AAAATCATGTATTTTCAAAA
82988 AAAATCATGTATTTTCAAA
1 AAAATCATGTATTTTCAAA
83007 GGGGTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAATCATGTATTTTCAAAA
Found at i:84409 original size:11 final size:12
Alignment explanation
Indices: 84379--84424 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 12
84369 TTGGTGCTGG
84379 AAACAAGATAAA
1 AAACAAGATAAA
* *
84391 AAATAAGAT-TA
1 AAACAAGATAAA
84402 AAACAAGATAAA
1 AAACAAGATAAA
*
84414 GAA-AAGATAAA
1 AAACAAGATAAA
84425 GAATTGCAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.72, C:0.04, G:0.11, T:0.13
Consensus pattern (12 bp):
AAACAAGATAAA
Found at i:84409 original size:23 final size:22
Alignment explanation
Indices: 84379--84421 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
84369 TTGGTGCTGG
84379 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
84402 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
84422 AAAGAATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:87684 original size:35 final size:35
Alignment explanation
Indices: 87644--87793 Score: 185
Period size: 35 Copynumber: 4.3 Consensus size: 35
87634 TACTATTTGT
* * * *
87644 TCATCACCATCTTCCATCACCTTTTTCAC-ACTATA
1 TCATCACCAACTTCCATCACC-ATTGCACGCCTATA
* *
87679 ACATCACCATCTTCCATCACCATTGCACGCCTATA
1 TCATCACCAACTTCCATCACCATTGCACGCCTATA
*
87714 TCATCACCAACTTCTATCACCATTGCACGCCTATA
1 TCATCACCAACTTCCATCACCATTGCACGCCTATA
* *
87749 TCATCACCAACTTCTATCACCATTTCACGCCTATA
1 TCATCACCAACTTCCATCACCATTGCACGCCTATA
* *
87784 TAACCACCAA
1 TCATCACCAA
87794 TCCCTTACCA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
34 5 0.05
35 99 0.95
ACGTcount: A:0.29, C:0.38, G:0.03, T:0.29
Consensus pattern (35 bp):
TCATCACCAACTTCCATCACCATTGCACGCCTATA
Found at i:88203 original size:6 final size:6
Alignment explanation
Indices: 88182--88223 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
88172 CAAAAAGAGA
88182 AAAAAG AAAGAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAAAG A
1 AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
88224 CTCCTACATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:88217 original size:16 final size:16
Alignment explanation
Indices: 88179--88223 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
88169 CAACAAAAAG
*
88179 AGAAAA-AAGAAAGAAG
1 AGAAAAGAA-AAAGAAA
88195 A-AAAAGAAAAAGAAA
1 AGAAAAGAAAAAGAAA
88210 AGAAAAGAAAAAGA
1 AGAAAAGAAAAAGA
88224 CTCCTACATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:93430 original size:13 final size:11
Alignment explanation
Indices: 93387--93468 Score: 51
Period size: 11 Copynumber: 6.9 Consensus size: 11
93377 CAATCTGTCA
93387 ATCACCATCATC
1 ATCACCAT-ATC
*
93399 A-CGCCTATATC
1 ATCACC-ATATC
*
93410 ATCGCCATAGTCC
1 ATCACCATA-T-C
93423 ATCACCATTATC
1 ATCACCA-TATC
*
93435 A-CGCCTATATC
1 ATCACC-ATATC
93446 ATCACCATATTCC
1 ATCACCATA-T-C
93459 ATCACCATAT
1 ATCACCATAT
93469 AACGCCTATA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.37
12 16 0.28
13 18 0.32
14 2 0.04
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (11 bp):
ATCACCATATC
Found at i:93436 original size:36 final size:36
Alignment explanation
Indices: 93387--93484 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 36
93377 CAATCTGTCA
* *
93387 ATCACCATCATCACGCCTATATCATCGCCATAGTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
*
93423 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
* *
93459 ATCACCA-TATAACGCCTATATTATCA
1 ATCACCATTATCACGCCTATATCATCA
93485 TCAACTTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 17 0.30
36 40 0.70
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCC
Found at i:97291 original size:13 final size:11
Alignment explanation
Indices: 97247--97331 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
97237 ACAATCTGTC
97247 CATCACCATCAT
1 CATCACCAT-AT
*
97259 CA-CGCCTATAT
1 CATCACC-ATAT
*
97270 CATCGCCATAGT
1 CATCACCATA-T
97282 CCATCACCATTAT
1 -CATCACCA-TAT
*
97295 CA-CGCCTATAT
1 CATCACC-ATAT
97306 CATCACCATATT
1 CATCACCATA-T
97318 CCATCACCATAT
1 -CATCACCATAT
97330 CA
1 CA
97332 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 23 0.38
12 17 0.28
13 18 0.30
14 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.27
Consensus pattern (11 bp):
CATCACCATAT
Found at i:97291 original size:36 final size:35
Alignment explanation
Indices: 97244--97348 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 35
97234 GATACAATCT
*
97244 GTCCATCACCATCATCACGCCTATATCATCGCCATA
1 GTCCATCACCAT-ATCACGCCTATATCATCACCATA
97280 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCA-TATCACGCCTATATCATCACCATA
* *
97316 TTCCATCACCATATCACGCCTATATTATCACCA
1 GTCCATCACCATATCACGCCTATATCATCACCA
97349 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 21 0.32
36 43 0.66
37 1 0.02
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.28
Consensus pattern (35 bp):
GTCCATCACCATATCACGCCTATATCATCACCATA
Found at i:99120 original size:13 final size:13
Alignment explanation
Indices: 99102--99159 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
99092 ACTATCTGTT
99102 CATCACCATCTTC
1 CATCACCATCTTC
*
99115 CATCACCAT-TTT
1 CATCACCATCTTC
* * **
99127 CA-CGCC-TATAA
1 CATCACCATCTTC
99138 CATCACCATCTTC
1 CATCACCATCTTC
99151 CATCACCAT
1 CATCACCAT
99160 TGCATGCCTA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 7 0.21
13 20 0.59
ACGTcount: A:0.28, C:0.41, G:0.02, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:99149 original size:36 final size:35
Alignment explanation
Indices: 99102--99204 Score: 138
Period size: 33 Copynumber: 3.0 Consensus size: 35
99092 ACTATCTGTT
99102 CATCACCATCTTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAA
* *
99138 CATCACCATCTTCCATCACCATTGCATGCCTAT-A
1 CATCACCATCTTCCATCACCATTTCACGCCTATAA
* * *
99172 -TTCACCAACTTCTATCACCATTTCACGCCTATA
1 CATCACCATCTTCCATCACCATTTCACGCCTATA
99205 TAACCACCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
33 27 0.46
34 1 0.02
35 10 0.17
36 21 0.36
ACGTcount: A:0.27, C:0.38, G:0.04, T:0.31
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAA
Found at i:99371 original size:15 final size:15
Alignment explanation
Indices: 99351--99391 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
99341 TCTTTGATAA
99351 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
99366 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
*
99381 CTATTCCTTTC
1 C-ATTTCTTTC
99392 TAATTATCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Done.